FASTA program discussion list

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Hi,
I am running into a problem with segmentation fault while using fasta through
another program (PASA, http://pasa.sourceforge.net). 

Here is the command and the error message:
fasta /tmp/50438.seq1 /tmp/50438.seq2 > /tmp/50438.grasta_result
Segmentation fault

The server I'm running on:
Linux rna 3.0.0 #1 SMP Thu Aug 4 15:10:31 CEST 2011 x86_64 Intel(R) Xeon(R) 
CPU
X7550 @ 2.00GHz GenuineIntel GNU/Linux

Fasta version: version 36.3.6 Sep, 2013(preload9)

Below is what the three files look like.

1. /tmp/50438.seq1:
>seq1
MNGPVDYIQEHTLKDVGAFMFTSESVGEGHPDKICDQISDAVLDAHLSQDPDAKVACETV
CKTGMVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQ
GVHLDRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPD
SKTQVTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEK
TVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAAR
WVAKSLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*

2. /tmp/50438.seq2:
>seq2
MVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQGVHL
DRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPDSKTQ
VTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEKTVYH
LQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAK
SLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*


3. /tmp/50438.grasta_result:
# fasta /tmp/50438.seq1 /tmp/50438.seq2
FASTA searches a protein or DNA sequence data bank
 version 36.3.6 Sep, 2013(preload9)
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: /tmp/50438.seq1
  1>>>seq1 - 342 aa
Library: /tmp/50438.seq2
    44997 residues in     1 sequences

Statistics: Altschul/Gish params: n0: 342 Lambda: 0.158 K: 0.019 H: 0.100
 statistics sampled from 0 (1) to 0 sequences
Algorithm: FASTA (3.8 Nov 2011) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.5), E-opt: 0.2 (0.5), width:  16
 Scan time:  0.040

The best scores are:                                      opt bits E(2)
seq2                                               (44997) 1854 429.0 2.2e-122
seq2                                               (44997)    0 6.9       2


Could someone explain why I get a segmentation fault? And how to get around it
so I can continue the PASA run?

Best regards,
Helena

Helena Storvall
PhD student
Sandberg lab
Karolinska Institutet
Stockholm, Sweden
email: